Through the widespread implementation of next-generation sequencing (NGS), analyses of the whole genome (the entire DNA content) and the whole transcriptome (the genes being expressed) are becoming commonplace. NGS enables the analysis of a vast amount of previously unattainable genetic information. Despite this potential, NGS has yet to be widely implemented in genetic studies of biological invasions. The study of the genomic causes and consequences of biological invasions allows a deeper understanding of the molecular mechanisms underpinning the invasion process. In this review, we present a brief introduction to NGS followed by a synthesis of current research in the genomics and transcriptomics of adaptation and colonization. We then highlight research opportunities in the field, including: (1) assembling genomes and transcriptomes of non-model organisms, (2) identifying genomic regions and candidate genes underlying evolutionary processes, and (3) studying the adaptive role of gene expression variation. In particular, because introduced species face a broad range of physiological and biotic challenges when colonizing novel and variable environments, transcriptomics will enable the study of gene regulatory pathways that may be responsible for acclimation or adaptation. To conclude, we identify a number of research approaches that will aid our future understanding of biological invasions [Current Zoology61 (3): 488–504, 2015 ].